I have a different theory about Merle.
Yes the Governor is pissed at him, but when they caught Daryl, he decided to stage the events in the pit, to set Merle up as the inside man in Rick's camp. He already knew Daryl and Merle were brothers when he was brought into the pit.
He will allow them to escape, even if it costs him a few more bodies, simply because he doesn't want these neighbors so close. He'll lose his control over some of the citizens of Woodbury if they think they can be safer at the prison.
When the Governor is through using Merle, then he will kill him.